added WDL2CWL conversion examples

[ambarishK]

This is my pull request for WDL2CWL conversion example.

Will fix https://github.com/common-workflow-library/bio-cwl-tools/issues/79

[mr-c]

Okay, the directory is restructured, but there are still many tool descriptions for tools that have descriptions for. So you need to try out the existing descriptions and either (1) propose changes or (2) motivate why a new description is needed.

Examples of (1) are : extra flag, additional output capture. Examples of (2) are: additional subcommand or fundamentally different mode of operation using an already described (sub)command.

[ambarishK]

Sir, I have run cwl-format on each of the tools.

[ambarishK]

GATK4 CreateSequenceDictionary tool - ReferenceSeqDictionaryDocker.cwl is generating error. Error is below.

ngsap2@ubuntu:~$ sudo docker run -v /var/run/docker.sock:/var/run/docker.sock -v "$PWD":"$PWD" -w="$PWD" commonworkflowlanguage/cwltool /home/ngsap2/GATK4Docker/ReferenceSeqDictionaryDockerNew.cwl --docker broadinstitute/gatk --ReferenceGenome /home/ngsap2/Downloads/testdata16march/ebola_ref.fasta --sampleName eb --gatk_path gatk
INFO /usr/local/bin/cwltool 2.0.20200107113851
INFO Resolved '/home/ngsap2/GATK4Docker/ReferenceSeqDictionaryDockerNew.cwl' to 'file:///home/ngsap2/GATK4Docker/ReferenceSeqDictionaryDockerNew.cwl'
INFO [job ReferenceSeqDictionaryDocker] /tmp/y7d6mg3o$ docker \
    run \
    -i \
    --volume=/tmp/y7d6mg3o:/PhuOQW:rw \
    --volume=/tmp/wb177ujt:/tmp:rw \
    --volume=/home/ngsap2/Downloads/testdata16march/ebola_ref.fasta:/var/lib/cwl/stg33a510ba-c3e7-4aee-9d06-a674f07f800a/ebola_ref.fasta:ro \
    --workdir=/PhuOQW \
    --read-only=true \
    --user=0:0 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/PhuOQW \
    --cidfile=/tmp/indc9ovr/20200517131951-916559.cid \
    docker \
    /bin/sh \
    -c \
    java -jar gatk CreateSequenceDictionary -R /var/lib/cwl/stg33a510ba-c3e7-4aee-9d06-a674f07f800a/ebola_ref.fasta -O eb.fasta.dict
/bin/sh: java: not found
INFO [job ReferenceSeqDictionaryDocker] Max memory used: 0MiB
ERROR [job ReferenceSeqDictionaryDocker] Job error:
("Error collecting output for parameter 'refDict':\nGATK4Docker/ReferenceSeqDictionaryDockerNew.cwl:27:5: Did not find output file with glob pattern: '['eb.fasta.dict']'", {})
WARNING [job ReferenceSeqDictionaryDocker] completed permanentFail
{}
WARNING Final process status is permanentFail